SAN FRANCISCO (AP) - Staring up at the sunny San Francisco sky, Marcus Thigpen peeked down at a pair of hard-charging defenders. By the time he looked back up, everything became blurry.

Same goes for the Miami Dolphins' season.

Thigpen's fumbled punt led to a 49ers touchdown that highlighted a series of mistakes in Miami's 27-13 loss Sunday at San Francisco. An ugly game that for so long seemed close ended the same way five of the last six have for the Dolphins: in defeat.

``I felt like I let the team down,'' Thigpen said.

That turned out to be a common phrase in the crammed quarters of Candlestick Park's visiting locker room.

Jonathan Freeny fielded a punt about the 2-yard line - then walked on the goal line for a touchback. Sean Smith was called for pass interference on a critical fourth-down play. Even worse, first-year Dolphins coach Joe Philbin challenged the seemingly clear-cut call on the field - and lost.

``We haven't mastered the concept of complementing one another,'' Philbin said. ``When we go down and kick a field goal, we give up a touchdown. We score a touchdown, they get another one. We didn't get a stop. We get a stop on defense (and) we get some momentum, we fumble a punt.''

That might sum up the Dolphins' demise this season.

Rookie Ryan Tannehill threw for 150 yards and a touchdown, and Reggie Bush ran for 65 yards on 14 carries against one of the league's most dominant defenses. Miami's makeshift offensive line only allowed two sacks - both to Aldon Smith, extending his league lead to 19 1/2 sacks - but Tannehill often had little time to throw.

The Dolphins defense didn't hold up, either.

Miami native and former Hurricanes standout Frank Gore ran for 63 yards and a touchdown to reach 1,000 yards rushing for the sixth time in his 49ers career. Anthony Dixon added another short TD run, and Colin Kaepernick ran for a late 50-yard touchdown after throwing for 185 yards in his fourth straight start since being promoted over Alex Smith.

The 49ers (9-3-1) held on to the No. 2 seed in the NFC behind Atlanta and mowed down another layer of Miami's playoff hopes in the process.

``None of us enjoy the situation that we're in right now,'' said Tannehill, who completed 17 of 33 passes. ``We don't enjoy losing. We don't enjoy preparing all week and not playing to our full potential on Sunday.''

The biggest bright spot for the Dolphins came when Anthony Fasano made a diving, one-handed touchdown catch for Miami (5-8) midway through the fourth quarter on a fourth down from the 3-yard line. The tight end's right knee landed in the end zone as he fell out of bounds under pressure from Donte Whitner to slice San Francisco's lead to 20-13 midway through the fourth quarter.

The Dolphins stopped the 49ers three-and-out on their next possession. Then Tannehill overthrew a tightly guarded Marlon Moore on the left sideline on fourth-and-10 from the 35 with 4:16 remaining before Kaepernick's long scoring run sealed San Francisco's victory.

``It's just a lack of playmaking at critical times. That's it,'' Philbin said.

The 49ers had no problem taking advantage of opportunities.

Thigpen fumbled trying to catch Andy Lee's punt early in the third quarter, C.J. Spillman recovered on the Dolphins 9 and Gore ran for a short TD two plays later to give Miami a 14-3 lead.

Aldon Smith lined up against rookie left tackle Jonathan Martin, a former Stanford star recruited by 49ers coach Jim Harbaugh. Martin shifted to the left side in place of Jake Long (left triceps), placed on season-ending injured reserve Tuesday. Smith and Martin shoved each other all day, jawed and even butted helmets.

``It got a little chippy, but that's how football goes,'' Martin said.

Dan Carpenter kicked a 53-yard field goal in the third quarter for the Dolphins and also an earlier 28-yarder. San Francisco outgained Miami 321 to 227 total yards.

The most costly chunk of that for the Dolphins came when officials whistled Sean Smith for pass interference on Michael Crabtree on fourth-and-1 from the 38 late in the third quarter. Five plays later, Dixon ran for his second touchdown of the season.

David Akers' 30-yard field goal in the second quarter tied the game at 3, then he kicked a 37-yarder as the first half expired to give the 49ers a 6-3 lead.

``We had some opportunities to put some more points on the board,'' Philbin said. ``We didn't. We were too generous.''

NOTES: Miami LB Koa Misi went down early in the third quarter with an ankle injury. ... The 49ers won nine games in back-to-back seasons for the first time since 2001-02. ... Under coach Jim Harbaugh, the 49ers improved to 3-0 against the AFC East and 6-1 vs. the AFC. ... 49ers LB Tavares Gooden sustained a rib injury.